glMDSPlot.DGEList {Glimma} | R Documentation

## Glimma MDS Plot

### Description

Draw an interactive MD plot from a DGEList object with distances calculated from most variable genes.

### Usage

    ## S3 method for class 'DGEList'
    glMDSPlot(
      x,
      top = 500,
      labels = NULL,
      groups = rep(1, ncol(x)),
      gene.selection = c("pairwise", "common"),
      prior.count = 2,
      main = "MDS Plot",
      path = getwd(),
      folder = "glimma-plots",
      html = "MDS-Plot",
      launch = TRUE,
      ...
    )

### Arguments

`x` | the DGEList containing the gene expressions.
`top` | the number of top most variable genes to use.
`labels` | the labels for each sample.
`groups` | the experimental group to which samples belong.
`gene.selection` | "pairwise" if most variable genes are to be chosen for each pair of samples or "common" to select the same genes for all comparisons.
`prior.count` | average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE.
`main` | the title of the plot.
`path` | the path in which the folder will be created.
`folder` | the name of the fold to save html file to.
`html` | the name of the html file to save plots to.
`launch` | TRUE to launch plot after call.
`...` | additional arguments.

### Value

Draws a two-panel interactive MDS plot in an html page. The left panel contains the plot between two MDS dimensions, with annotations displayed on hover. The right panel contains a bar plot of the eigenvalues of each dimension, clicking on any of the bars will plot the corresponding dimension against the next dimension.

### Author(s)

Shian Su, Gordon Smyth

[Package Glimma version 2.0.0 Index]